Are you comparing the same airlines ?
Just wondering, because not all airlines are created equal when it comes to what is included in the cost. If you are comparing, say, Jetblue from Buffalo with Spirit from Detroit then there are huge difference in inclusions. Jetblue includes free seat selection, a free checked bag per person, free snacks, TV's on each seat, the ability to get a credit if your flight price declines, free carry on bag, etc. Spirit charges you for everything. That would definitely be a consideration.
I don't think your flight prices are that out of line

(maybe I am weird). Our family size is the same as yours (your toddler and my teenager take up the same amount of space.....one seat.....so we are both still pricing out 3 seats on the plane). We paid $1000 return from Syracuse in January 2012, $868 return from Syracuse in August 2012, and $1125 return from Buffalo in December 2012. January and August were Jetblue both directions, December was Airtran there and Jetblue home. So your $1000 quote is pretty much in line with what we have been paying from the NY airports.
We have been pricing out the last week of August 2013, and so far, we are looking at $1019 return from Syracuse on Jetblue. Comparing against, say, Westjet from Toronto, its a steal.